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Items: 1 to 20 of 116

1.

Determining the minimum number of protein-protein interactions required to support known protein complexes.

Nakajima N, Hayashida M, Jansson J, Maruyama O, Akutsu T.

PLoS One. 2018 Apr 26;13(4):e0195545. doi: 10.1371/journal.pone.0195545. eCollection 2018.

2.

Comparative analysis and assessment of M. tuberculosis H37Rv protein-protein interaction datasets.

Zhou H, Wong L.

BMC Genomics. 2011 Nov 30;12 Suppl 3:S20. doi: 10.1186/1471-2164-12-S3-S20. Epub 2011 Nov 30.

3.

L-GRAAL: Lagrangian graphlet-based network aligner.

Malod-Dognin N, Pržulj N.

Bioinformatics. 2015 Jul 1;31(13):2182-9. doi: 10.1093/bioinformatics/btv130. Epub 2015 Feb 28.

4.

Protein complex prediction via verifying and reconstructing the topology of domain-domain interactions.

Ozawa Y, Saito R, Fujimori S, Kashima H, Ishizaka M, Yanagawa H, Miyamoto-Sato E, Tomita M.

BMC Bioinformatics. 2010 Jun 28;11:350. doi: 10.1186/1471-2105-11-350.

5.

MEGADOCK-Web: an integrated database of high-throughput structure-based protein-protein interaction predictions.

Hayashi T, Matsuzaki Y, Yanagisawa K, Ohue M, Akiyama Y.

BMC Bioinformatics. 2018 May 8;19(Suppl 4):62. doi: 10.1186/s12859-018-2073-x.

6.

PathPPI: an integrated dataset of human pathways and protein-protein interactions.

Tang H, Zhong F, Liu W, He F, Xie H.

Sci China Life Sci. 2015 Jun;58(6):579-89. doi: 10.1007/s11427-014-4766-3. Epub 2015 Jan 15.

PMID:
25591449
7.

Constructing a robust protein-protein interaction network by integrating multiple public databases.

Martha VS, Liu Z, Guo L, Su Z, Ye Y, Fang H, Ding D, Tong W, Xu X.

BMC Bioinformatics. 2011 Oct 18;12 Suppl 10:S7. doi: 10.1186/1471-2105-12-S10-S7.

8.

PCDq: human protein complex database with quality index which summarizes different levels of evidences of protein complexes predicted from h-invitational protein-protein interactions integrative dataset.

Kikugawa S, Nishikata K, Murakami K, Sato Y, Suzuki M, Altaf-Ul-Amin M, Kanaya S, Imanishi T.

BMC Syst Biol. 2012;6 Suppl 2:S7. doi: 10.1186/1752-0509-6-S2-S7. Epub 2012 Dec 12.

9.

Geometric de-noising of protein-protein interaction networks.

Kuchaiev O, Rasajski M, Higham DJ, Przulj N.

PLoS Comput Biol. 2009 Aug;5(8):e1000454. doi: 10.1371/journal.pcbi.1000454. Epub 2009 Aug 7.

10.

RocSampler: regularizing overlapping protein complexes in protein-protein interaction networks.

Maruyama O, Kuwahara Y.

BMC Bioinformatics. 2017 Dec 6;18(Suppl 15):491. doi: 10.1186/s12859-017-1920-5.

11.

Identifying protein complexes by reducing noise in interaction networks.

Liao B, Fu X, Cai L, Chen H.

Protein Pept Lett. 2014 Jul;21(7):688-95.

PMID:
24654850
12.

Detecting Protein Complexes Based on Uncertain Graph Model.

Zhao B, Wang J, Li M, Wu FX, Pan Y.

IEEE/ACM Trans Comput Biol Bioinform. 2014 May-Jun;11(3):486-97. doi: 10.1109/TCBB.2013.2297915.

PMID:
26356017
13.

Sampling strategy for protein complex prediction using cluster size frequency.

Tatsuke D, Maruyama O.

Gene. 2013 Apr 10;518(1):152-8. doi: 10.1016/j.gene.2012.11.050. Epub 2012 Dec 9.

PMID:
23235119
14.

ConnectedAlign: a PPI network alignment method for identifying conserved protein complexes across multiple species.

Gao J, Song B, Hu X, Yan F, Wang J.

BMC Bioinformatics. 2018 Aug 13;19(Suppl 9):286. doi: 10.1186/s12859-018-2271-6.

15.

Prediction of Protein Interactions by Structural Matching: Prediction of PPI Networks and the Effects of Mutations on PPIs that Combines Sequence and Structural Information.

Tuncbag N, Keskin O, Nussinov R, Gursoy A.

Methods Mol Biol. 2017;1558:255-270. doi: 10.1007/978-1-4939-6783-4_12.

PMID:
28150242
16.

MOEPGA: A novel method to detect protein complexes in yeast protein-protein interaction networks based on MultiObjective Evolutionary Programming Genetic Algorithm.

Cao B, Luo J, Liang C, Wang S, Song D.

Comput Biol Chem. 2015 Oct;58:173-81. doi: 10.1016/j.compbiolchem.2015.06.006. Epub 2015 Jul 7.

PMID:
26298638
17.
18.

Finding low-conductance sets with dense interactions (FLCD) for better protein complex prediction.

Wang Y, Qian X.

BMC Syst Biol. 2017 Mar 14;11(Suppl 3):22. doi: 10.1186/s12918-017-0405-5.

19.

Homology-based prediction of interactions between proteins using Averaged One-Dependence Estimators.

Murakami Y, Mizuguchi K.

BMC Bioinformatics. 2014 Jun 23;15:213. doi: 10.1186/1471-2105-15-213.

20.

Protein complex prediction based on simultaneous protein interaction network.

Jung SH, Hyun B, Jang WH, Hur HY, Han DS.

Bioinformatics. 2010 Feb 1;26(3):385-91. doi: 10.1093/bioinformatics/btp668. Epub 2009 Dec 4.

PMID:
19965885

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